Abstract
dc:description.abstractMutations accumulate in all cells throughout life from the very first cell division of the fertilised egg. These somatic mutations contribute to cancer and other diseases as well as provide insights into ageing and development. Although somatic mutations in cancer genomes have been extensively studied for the past two decades, because of technological limitations, we are still in the process of understanding patterns of somatic mutation in normal cells. This accumulation of somatic mutations is shaped by numerous mutational processes, each generating a distinctive profile of mutations, called a ‘mutational signature’. From mutational signatures, one can infer a history of operating mutational processes that have acted on the genome. Therefore, they can be a useful tool in revealing the historical presence of mutational processes in tissues that may be linked to causes of diseases. During my PhD, I first characterised the operating mutational processes in normal human small intestine through extensive sequencing and phylogenetic reconstruction of multiple biopsies from a group of 39 individuals within UK. Subsequently, I demonstrated how mutational signatures in normal tissues can be used for global surveillance of mutagenic exposures that may cause cancer, through a collection of normal kidneys from more than 200 individuals from multiple geographic regions. The small intestine epithelium is thought to be one of the most vigorously self-renewing tissues of adult mammals. The base of each small intestinal crypt is occupied by stem cells and the descendants of a single recent ancestor stem cell comprise most cells in each crypt. Therefore, isolation of single crypts provides relatively homogeneous clones of cells from which somatic mutations can be called. Using laser-capture microdissection to isolate individual crypts followed by whole-genome sequencing, I characterised somatic mutation rates and mutational signatures in the small intestine, and identified the frequent presence of a mutational process commonly found in cancer, which could be explained by collateral damage caused by an RNA editing enzyme involved in lipid transportation. On the contrary, normal kidney tissue is polyclonal, maintained largely by quiescent cells with low turnover. Because homogeneous clones cannot be easily isolated, a high-accuracy duplex sequencing approach was applied to distinguished somatic mutations from random sequencing errors. DNA extracts from normal kidney cortex was collected from nine countries with varying kidney cancer incidence rates, and mutational signature analysis revealed geographical variation in types and contributions of mutational signatures, resulting from both known and unknown environmental exposures. In addition, I used laser-microdissection to isolate and then sequenced distinct microscopic structures within the normal kidney, including glomeruli, proximal tubules, distal tubules and medulla, to estimate an accurate somatic mutation rate of these structures and how they are affected by different environmental exposures. Together, these two studies describe the distinct somatic mutation landscapes among different normal human tissues with active cell division and low cell division rates, as well as the same type of tissues collected from different geographic regions. These findings inform us about the varying patterns and mechanisms of mutational processes in normal human tissues, demonstrate how normal tissues can provide new insights into mutational processes, and exemplify how normal tissues can be used to identify geographically variable mutagenic exposures.
Degree
thesis:*- Name dc:type.qualificationname
- Doctor of Philosophy (PhD)
- Level dc:type.qualificationlevel
- Doctoral
- Grantor dc:publisher.institution
- University of Cambridge
- Year dc:date.issued
- 2024
Author and committee
dc:creator, dc:contributor.*- Author dc:creator
-
- Wang, Yichen
- Advisors dc:contributor.advisor
-
- Stratton, Michael
- Campbell, Peter
Subjects
dc:subject × 6Rights
dc:rightsIdentifiers
dc:identifier.*- DOI dc:identifier.doi
- https://doi.org/10.17863/CAM.113024
- OAI identifier oai:identifier
- oai:www.repository.cam.ac.uk:1810/375296